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- PDB-2mub: Solution structure of the analgesic sea anemone peptide APETx2 -

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Basic information

Entry
Database: PDB / ID: 2mub
TitleSolution structure of the analgesic sea anemone peptide APETx2
ComponentsToxin APETx2
KeywordsTOXIN / Disulfide-rich toxin / Defensin fold / ASIC3 blocker
Function / homology
Function and homology information


nematocyst / ion channel inhibitor activity / sodium channel regulator activity / potassium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
BDS potassium channel toxin / Potassium-channel blocking toxin / Anthopleurin-A / Myotoxin/Anemone neurotoxin domain superfamily / Anthopleurin-A / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Biological speciesAnthopleura elegantissima (clonal anemone)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMobli, M. / King, G.F. / Rosengren, K.J. / Jensen, J.E.
Citation
Journal: J.Med.Chem. / Year: 2014
Title: Understanding the Molecular Basis of Toxin Promiscuity: The Analgesic Sea Anemone Peptide APETx2 Interacts with Acid-Sensing Ion Channel 3 and hERG Channels via Overlapping Pharmacophores.
Authors: Jensen, J.E. / Cristofori-Armstrong, B. / Anangi, R. / Rosengren, K.J. / Lau, C.H. / Mobli, M. / Brust, A. / Alewood, P.F. / King, G.F. / Rash, L.D.
#1: Journal: Protein Sci. / Year: 2005
Title: Solution structure of APETx2, a specific peptide inhibitor of ASIC3 proton-gated channels.
Authors: Chagot, B. / Escoubas, P. / Diochot, S. / Bernard, C. / Lazdunski, M. / Darbon, H.
#2: Journal: Toxicon / Year: 2009
Title: Chemical synthesis and folding of APETx2, a potent and selective inhibitor of acid sensing ion channel 3.
Authors: Jensen, J.E. / Durek, T. / Alewood, P.F. / Adams, D.J. / King, G.F. / Rash, L.D.
History
DepositionSep 7, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Structure summary
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toxin APETx2


Theoretical massNumber of molelcules
Total (without water)4,5711
Polymers4,5711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100Best MolProbity score
RepresentativeModel #1best stereochemistry

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Components

#1: Protein/peptide Toxin APETx2


Mass: 4571.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Anthopleura elegantissima (clonal anemone) / References: UniProt: P61542
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H COSY
1412D 1H-1H NOESY
1512D 1H-1H TOCSY

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Sample preparation

DetailsContents: 300 uM APETx2, 20 mM potassium phosphate, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
300 uMAPETx2-11
20 mMpotassium phosphate-21
Sample conditionsIonic strength: 20 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
TALOS+Cornilescu, Delaglio and Baxdata analysis
TopSpin3.1Cornilescu, Delaglio and Baxprocessing
TopSpin3.1Cornilescu, Delaglio and Baxcollection
Rowland_NMR_Toolkit3J. C. Hoch & A. S. Sternprocessing
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: AUTOMATED NOE ASSIGNMENTS BY CYANA
NMR constraintsNOE constraints total: 569 / NOE intraresidue total count: 156 / NOE long range total count: 186 / NOE medium range total count: 72 / NOE sequential total count: 155 / Protein chi angle constraints total count: 12 / Protein phi angle constraints total count: 41 / Protein psi angle constraints total count: 14
NMR representativeSelection criteria: best stereochemistry
NMR ensembleConformer selection criteria: Best MolProbity score / Conformers calculated total number: 100 / Conformers submitted total number: 20

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